GWideCodeML

GWideCodeML performs genome-wide evolutionary hypothesis testing by orchestrating codeml (PAML) analyses across many gene alignments to detect selection and compare evolutionary models.

Key Features:

• Codeml (PAML) integration: Executes the codeml program from the PAML suite to perform molecular evolution analyses such as detection of positive selection.
• Genome-wide parallelization: Runs codeml analyses in parallel to scale from single-gene to genome-wide studies.
• Automatic tree pruning: Prunes phylogenetic trees automatically to accommodate varying taxon sets for individual gene alignments.
• Flexible taxon handling: Processes alignments with differing numbers of taxa, enabling inclusion of genes lacking strict one-to-one orthology.
• Python implementation: Implemented as a Python package that coordinates per-gene codeml analyses and tree adjustments.

Scientific Applications:

• Detection of positive selection: Identifies genes or sites under positive selection using codeml model comparisons.
• Comparative genomics: Enables large-scale comparisons of selection pressures across genomes by maximizing the number of genes analyzed.
• Phylogenetic analyses: Facilitates phylogeny-aware evolutionary hypothesis testing by adapting trees to available taxa per alignment.
• Genome-wide evolutionary hypothesis testing: Supports broad testing of evolutionary models across many loci rather than single-gene analyses.

Methodology:

Coordinates per-gene codeml (PAML) runs executed in parallel, automatically prunes phylogenetic trees to match taxa in each alignment, and is implemented as a Python package.